On Aug 18, 2008, at 10:07 PM, Ben Webb wrote:
> Daniel Russel wrote: >> You should read the emails on imp-dev occasionally :-) > > Indeed. > >> Anyway, that method should definitely not be made public as it isn't >> guaranteed to do anything useful. For some of the restraints >> (NonbondedRestraints) it returns nothing and for others, such as the >> PairListRestraint it globs together lots of particles which aren't >> actually interacting. >> >> The best solution is probably to add a new virtual method >> get_interacting_pairs which returns a list of interacting particle >> pairs (since I think that is what you want). Or something similar. It >> would be quite easy to implement for existing restraints. > > Agreed. I seem to recall that's what you suggested the last time Keren > asked this question. I think I agreed that time around too. ;) funny !! ;) > > > Keren, what is your use case? If it's not "get a list of interacting > pairs" then we'll need to do something different. Ben - as I wrote in my last reply - it is not all_pairs, since the optimization tries to find that. We get MSMS data which says a,b,c,d,e create a complex - but we do not know which interacts with which. so what DOMINO needs out of the restraint is a-e .
> > > Ben > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev